-/*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
* This file is part of Jalview.
- *
+ *
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- *******************************************************************************/
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
+import jalview.util.MessageManager;
+
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
*
* @version $Revision$ $Date$
*/
-public class Sequence extends jalview.schemabinding.version2.SequenceType
-implements java.io.Serializable
+public class Sequence extends jalview.schemabinding.version2.SequenceType
+ implements java.io.Serializable
{
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * dataset sequence id for this sequence. Will be created as
- * union of sequences.
- *
- */
- private java.lang.String _dsseqid;
-
- /**
- * Field _DBRefList.
- */
- private java.util.Vector _DBRefList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Sequence() {
- super();
- this._DBRefList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vDBRef
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addDBRef(
- final jalview.schemabinding.version2.DBRef vDBRef)
- throws java.lang.IndexOutOfBoundsException {
- this._DBRefList.addElement(vDBRef);
- }
-
- /**
- *
- *
- * @param index
- * @param vDBRef
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addDBRef(
- final int index,
- final jalview.schemabinding.version2.DBRef vDBRef)
- throws java.lang.IndexOutOfBoundsException {
- this._DBRefList.add(index, vDBRef);
- }
-
- /**
- * Method enumerateDBRef.
- *
- * @return an Enumeration over all
- * jalview.schemabinding.version2.DBRef elements
- */
- public java.util.Enumeration enumerateDBRef(
- ) {
- return this._DBRefList.elements();
- }
-
- /**
- * Method getDBRef.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * jalview.schemabinding.version2.DBRef at the given index
- */
- public jalview.schemabinding.version2.DBRef getDBRef(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._DBRefList.size()) {
- throw new IndexOutOfBoundsException("getDBRef: Index value '" + index + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");
- }
-
- return (jalview.schemabinding.version2.DBRef) _DBRefList.get(index);
- }
-
- /**
- * Method getDBRef.Returns the contents of the collection in an
- * Array. <p>Note: Just in case the collection contents are
- * changing in another thread, we pass a 0-length Array of the
- * correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.DBRef[] getDBRef(
- ) {
- jalview.schemabinding.version2.DBRef[] array = new jalview.schemabinding.version2.DBRef[0];
- return (jalview.schemabinding.version2.DBRef[]) this._DBRefList.toArray(array);
- }
-
- /**
- * Method getDBRefCount.
- *
- * @return the size of this collection
- */
- public int getDBRefCount(
- ) {
- return this._DBRefList.size();
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * dataset sequence id for this sequence. Will be created as union of
+ * sequences.
+ *
+ */
+ private java.lang.String _dsseqid;
+
+ /**
+ * Field _DBRefList.
+ */
+ private java.util.Vector _DBRefList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Sequence()
+ {
+ super();
+ this._DBRefList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vDBRef
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addDBRef(final jalview.schemabinding.version2.DBRef vDBRef)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._DBRefList.addElement(vDBRef);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vDBRef
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addDBRef(final int index,
+ final jalview.schemabinding.version2.DBRef vDBRef)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._DBRefList.add(index, vDBRef);
+ }
+
+ /**
+ * Method enumerateDBRef.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.DBRef
+ * elements
+ */
+ public java.util.Enumeration enumerateDBRef()
+ {
+ return this._DBRefList.elements();
+ }
+
+ /**
+ * Method getDBRef.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.DBRef at the given
+ * index
+ */
+ public jalview.schemabinding.version2.DBRef getDBRef(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._DBRefList.size())
+ {
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getDBRef",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._DBRefList.size() - 1)).toString()
+ }));
}
- /**
- * Returns the value of field 'dsseqid'. The field 'dsseqid'
- * has the following description: dataset sequence id for this
- * sequence. Will be created as union of sequences.
- *
- *
- * @return the value of field 'Dsseqid'.
- */
- public java.lang.String getDsseqid(
- ) {
- return this._dsseqid;
+ return (jalview.schemabinding.version2.DBRef) _DBRefList.get(index);
+ }
+
+ /**
+ * Method getDBRef.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.DBRef[] getDBRef()
+ {
+ jalview.schemabinding.version2.DBRef[] array = new jalview.schemabinding.version2.DBRef[0];
+ return (jalview.schemabinding.version2.DBRef[]) this._DBRefList
+ .toArray(array);
+ }
+
+ /**
+ * Method getDBRefCount.
+ *
+ * @return the size of this collection
+ */
+ public int getDBRefCount()
+ {
+ return this._DBRefList.size();
+ }
+
+ /**
+ * Returns the value of field 'dsseqid'. The field 'dsseqid' has the following
+ * description: dataset sequence id for this sequence. Will be created as
+ * union of sequences.
+ *
+ *
+ * @return the value of field 'Dsseqid'.
+ */
+ public java.lang.String getDsseqid()
+ {
+ return this._dsseqid;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllDBRef(
- ) {
- this._DBRefList.clear();
- }
-
- /**
- * Method removeDBRef.
- *
- * @param vDBRef
- * @return true if the object was removed from the collection.
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
*/
- public boolean removeDBRef(
- final jalview.schemabinding.version2.DBRef vDBRef) {
- boolean removed = _DBRefList.remove(vDBRef);
- return removed;
+ public void removeAllDBRef()
+ {
+ this._DBRefList.clear();
+ }
+
+ /**
+ * Method removeDBRef.
+ *
+ * @param vDBRef
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeDBRef(
+ final jalview.schemabinding.version2.DBRef vDBRef)
+ {
+ boolean removed = _DBRefList.remove(vDBRef);
+ return removed;
+ }
+
+ /**
+ * Method removeDBRefAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.DBRef removeDBRefAt(final int index)
+ {
+ java.lang.Object obj = this._DBRefList.remove(index);
+ return (jalview.schemabinding.version2.DBRef) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vDBRef
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setDBRef(final int index,
+ final jalview.schemabinding.version2.DBRef vDBRef)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._DBRefList.size())
+ {
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setDBRef",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._DBRefList.size() - 1)).toString()
+ }));
}
- /**
- * Method removeDBRefAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.DBRef removeDBRefAt(
- final int index) {
- java.lang.Object obj = this._DBRefList.remove(index);
- return (jalview.schemabinding.version2.DBRef) obj;
- }
-
- /**
- *
- *
- * @param index
- * @param vDBRef
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setDBRef(
- final int index,
- final jalview.schemabinding.version2.DBRef vDBRef)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._DBRefList.size()) {
- throw new IndexOutOfBoundsException("setDBRef: Index value '" + index + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");
- }
-
- this._DBRefList.set(index, vDBRef);
- }
-
- /**
- *
- *
- * @param vDBRefArray
- */
- public void setDBRef(
- final jalview.schemabinding.version2.DBRef[] vDBRefArray) {
- //-- copy array
- _DBRefList.clear();
-
- for (int i = 0; i < vDBRefArray.length; i++) {
- this._DBRefList.add(vDBRefArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'dsseqid'. The field 'dsseqid' has
- * the following description: dataset sequence id for this
- * sequence. Will be created as union of sequences.
- *
- *
- * @param dsseqid the value of field 'dsseqid'.
- */
- public void setDsseqid(
- final java.lang.String dsseqid) {
- this._dsseqid = dsseqid;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.SequenceType
- */
- public static jalview.schemabinding.version2.SequenceType unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.SequenceType) Unmarshaller.unmarshal(jalview.schemabinding.version2.Sequence.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+ this._DBRefList.set(index, vDBRef);
+ }
+
+ /**
+ *
+ *
+ * @param vDBRefArray
+ */
+ public void setDBRef(
+ final jalview.schemabinding.version2.DBRef[] vDBRefArray)
+ {
+ // -- copy array
+ _DBRefList.clear();
+
+ for (int i = 0; i < vDBRefArray.length; i++)
+ {
+ this._DBRefList.add(vDBRefArray[i]);
}
+ }
+
+ /**
+ * Sets the value of field 'dsseqid'. The field 'dsseqid' has the following
+ * description: dataset sequence id for this sequence. Will be created as
+ * union of sequences.
+ *
+ *
+ * @param dsseqid
+ * the value of field 'dsseqid'.
+ */
+ public void setDsseqid(final java.lang.String dsseqid)
+ {
+ this._dsseqid = dsseqid;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.SequenceType
+ */
+ public static jalview.schemabinding.version2.SequenceType unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.SequenceType) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.Sequence.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}